Abstract

Cyclic diguanylic acid (CDG) is a ubiquitous messenger involved in bacterial signaling networks. Despite its central role in motility, biofilm formation, virulence, and flagellum development, fundamental properties such as its aggregation state are still poorly understood. Here the dynamics and stability of metal-free and Mg2+-bound CDG are characterized. Atomistic simulations establish that the CDG dimer is slightly favored (by −5 kcal mol−1) over its dissociated form (2 CDG), while the Mg2+ ion coordinated in the X-ray structure readily dissociates from (CDG)2 in solution and prefers water coordination. As a ligand in a protein, CDG binds both as a U-shaped and a quasilinear monomer. The current results indicate that the energy difference between these two conformations is only a few kilocalories per mole, which explains the facile adaptation to different protein environments. This, together with the slight preference of (CDG)2 over 2 CDG suggests that (CDG)2 binding to a protein does probably not occur via sequential binding of two individual monomers.